Nothing I had done with toggling the setting in PathFinder and restarting worked (I literally spent over 2 hours trying different combinations of toggling the setting, restarting apps, and restarting my computer).
But based on your statement about modifying the setting file, I looked into it and I found something which does work:
Quit Alfred 2
Open ~/Library/Preferences/com.runningwithcrayons.Alfred-2.plist (this file is a binary property list, so you'll need a plist viewer - I'm using Xcode)
Under Root (where everything is), add a key called NSFileViewer of type String with the value com.cocoatech.PathFinder
Repeat the process for ~/Library/Preferences/com.runningwithcrayons.Alfred-Preferences.plist - just to be sure
Restart Alfred 2 and everything will be working as you expect.